Alignments for a candidate for ofo in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Rhizorhabdus wittichii RW1

Align branched-chain ketoacid ferredoxin reductase (EC 1.2.7.7) active on 4-methyl-2-oxopentanoate, (S)-3-methyl-2-oxopentanoate, or 3-methyl-2-oxobutanoate (characterized)
to candidate WP_011952018.1 SWIT_RS05980 indolepyruvate ferredoxin oxidoreductase family protein

Query= reanno::psRCH2:GFF3452
         (1156 letters)



>NCBI__GCF_000016765.1:WP_011952018.1
          Length = 1157

 Score = 1060 bits (2742), Expect = 0.0
 Identities = 571/1157 (49%), Positives = 749/1157 (64%), Gaps = 21/1157 (1%)

Query: 6    IRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDKSLW 65
            + LD  Y    G  ++TG QAL RLPM+Q + D+  GLNT G ++GYRGSPLG  D+ LW
Sbjct: 7    VSLDSIYGAEEGPSFMTGIQALVRLPMMQRRLDRRNGLNTAGLVTGYRGSPLGAYDQQLW 66

Query: 66   EARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRAGDV 125
            +A  YL  H I FQPG+NE+LAATA+WG+Q    F   + DGVF +WYGKG GVDR GDV
Sbjct: 67   KASKYLDAHDIVFQPGLNEDLAATALWGAQMHRAFGRTRADGVFGIWYGKGNGVDRTGDV 126

Query: 126  FKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDYGII 185
            F++AN  G +P GGVL + GDDH  +SS  PHQ++  F +  +PV+ PA V EIL  G+ 
Sbjct: 127  FRNANVLGTAPLGGVLAIGGDDHAAQSSMFPHQTDGIFQSVMMPVIQPATVGEILSLGLA 186

Query: 186  GWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVH----IRWPDP 241
            G+ LSR+SG WVA+KTIAE V+S+A  E+     +   P +  +P  G++    + WP  
Sbjct: 187  GFALSRFSGLWVAMKTIAEVVESAASFELPDSYPRFISPAE-AVPAHGLNWDPRVAWPAQ 245

Query: 242  PLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDE 301
                E+R+   ++ A  A+ARAN ++R +L     RL ++T GK++ DV QAL +LG+DE
Sbjct: 246  RTELERRMIEERLPAVTAWARANEIDRPVLQGGGRRLCVVTVGKAHQDVMQALANLGIDE 305

Query: 302  ALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKR 361
                ++GL V KV MSWPL+  S+  FA G +EILVVEEKR ++E+Q+   L+N     R
Sbjct: 306  GGARAIGLSVYKVAMSWPLDSASLLAFADGFEEILVVEEKRPVVEEQVKVALFNRS-GAR 364

Query: 362  PRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAAR 421
            PRV G+ D +G +LLP   E  P M+AR I  RL    T+D + ARLA + A+       
Sbjct: 365  PRVTGKTDAEGRALLPQTLEFDPLMVARAIVGRLPG--TAD-LAARLAAIEARVPTGEVV 421

Query: 422  SYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYM-VQWMDRRTETFTQMGGEGVNWI 480
             +   R P +CSGCPHNSSTK PEGS A  GIGCH M V     +T TF+QMGGEG+ W+
Sbjct: 422  PFPA-RKPFFCSGCPHNSSTKTPEGSIAGGGIGCHVMAVSQPKLKTATFSQMGGEGLQWV 480

Query: 481  GQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGEL 540
            G APF++T H+FQNLGDGTY HSG LA+RAAVAA  N+T+KILYNDAVAMTGGQP +G +
Sbjct: 481  GAAPFSETGHIFQNLGDGTYQHSGLLAIRAAVAAKANITFKILYNDAVAMTGGQPAEGAI 540

Query: 541  RVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSV 600
               ++SRQ+  EGV +I LVSD+PD++ +    A   +  HR +LD VQR LRE  GV+ 
Sbjct: 541  DPARISRQLAAEGVGQIHLVSDDPDRWRAAPDLAEGVTIAHRDDLDRVQRRLREVPGVTA 600

Query: 601  IIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKR 660
            IIY+QTCA EKRRRRKRG+  DP KR FINP VCEGCGDC  +SNC+AV PLET  GRKR
Sbjct: 601  IIYEQTCAAEKRRRRKRGEFPDPDKRIFINPRVCEGCGDCSVQSNCIAVEPLETGFGRKR 660

Query: 661  EIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAV-AGGIEA---ATLPEPQHPTLDRPW 716
             I+Q++CNKDFSC++GFCPSFV V G  LRKP+       EA   A LPEP+ P  D   
Sbjct: 661  RINQSSCNKDFSCIKGFCPSFVEVEGAVLRKPDGERLKAFEASRFAALPEPERPARDGVA 720

Query: 717  NVLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYA 776
            N+ + G+GG GV T+GALLG AAHL+G+G TVLD  GLAQK G V + VRIA     I+A
Sbjct: 721  NIYVAGIGGLGVLTIGALLGTAAHLDGRGATVLDFTGLAQKNGAVVSQVRIAPPGVPIHA 780

Query: 777  VRIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAM 836
            VRI AGE D+LLG D++VAAG + L R+    S  V+N  E+ TA+   + D  +PGAAM
Sbjct: 781  VRIGAGEIDVLLGTDMVVAAGQDVLRRIAADRSVLVLNDDETPTADVVTDRDFALPGAAM 840

Query: 837  RQAISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELN 896
               ++    A  TH + AT +A  L G+++A N  LLG A+Q+GL+P+ AEA+  AI  N
Sbjct: 841  ADTLTRRARA--THRLRATSIAEGLFGNNVAANTLLLGHAWQKGLIPLDAEAVRGAIRAN 898

Query: 897  GVSAKLNLQAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGL 956
            G +  LNL+AF WGR A ++   VE++A  +    P  +T++ +       LT YQ A  
Sbjct: 899  GAAVSLNLRAFDWGRLAAIDLALVEEMA-GLAAPAPQTETIDALAARLAAELTAYQDARY 957

Query: 957  ARRYRQLVERVRDADSA---DDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEA 1013
            A R+  LV   R A +    +    ++AVAR  ++L+AYKDEYEVARL+++P F   L  
Sbjct: 958  AARFAALVAAARRAAAGLGREGEDFAEAVARNAYRLMAYKDEYEVARLHADPAFAATLGE 1017

Query: 1014 QFEGDYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYG 1073
            QF    +L  +LAP  L++ DP TG PRKR  GPW+   F +LA+ + LRG+  DPFG+ 
Sbjct: 1018 QFSDRRRLSVYLAPPLLSRIDPATGRPRKRRFGPWIFTAFRLLARMKGLRGSWADPFGHS 1077

Query: 1074 HDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKARQQE 1133
            H+RR ERQLI +Y   V EL A L P     A  +A LP+ IRGYGPVK  +IA+A  ++
Sbjct: 1078 HERRTERQLIEDYVALVGELAADLSPATLPIATELARLPDAIRGYGPVKAAAIAEAEARK 1137

Query: 1134 KLLREQLAKGDEVQSVR 1150
              L E LA+       R
Sbjct: 1138 ATLLEALAESRRPSEAR 1154


Lambda     K      H
   0.319    0.136    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2851
Number of extensions: 113
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1156
Length of database: 1157
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1110
Effective search space:  1230990
Effective search space used:  1230990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources